Vid Luther has a new post to his blog showing how to switch the storage engine only one (or any number of individual tables) in your MySQL-backed Propel/Symfony project.
I need one MyISAM table in my schema, I'm using Symfony 1.2 and Propel 1.3. As flexible as Symfony and it's YAML files are, Propel currently doesn't allow you to change the storage engine on the fly. [...] So, the next best thing to do now is to have it so that when Symfony runs propel:insert-sql, I can piggyback my own SQL to it. Luckily, this is possible, and it's explained here.
He gives an example of how he's doing it - making a simple alter table script, putting it into a SQL file and pushing it out into the project's setup via a "propel:insert:sql" command.